1. Antonio Laganà University of Perugia (UNIPG), IT
TOWARDS A VIRTUAL RESEARCH COMMUNITY FOR CHEMISTRY, MOLECULAR AND MATERIALS SCIENCE & TECHNOLOGIES
Antonio Laganà University of Perugia (UNIPG), IT
CMMST: A VIRTUAL TEAM OF 24 Researchers, 12 countries 1

2. MAIN FEATURES 1) PORTALS FOR SHARING RESOURCES, TOOLS
2) WORKFLOWS FOR COMPOSING MODULES OF COMPLEX APPLICATIONS
3) COLLABORATE IN JOINT ENDEAVOURS
4) QOS AND QOU AND CREDIT SYSTEM
5) DATA FORMATS (Q5 and D5)
6) DATA WORKFLOWS (HTC-HPC elaboration)
7) DATA MANAGEMENT TOOLS (data location, registration, access, movement, storage and persistency) FOR APPLICATIONS
8) DISTRIBUTED KNOWLEDGE (Production, accumulation and transfer) FOR RESEARCH, TRAINING AND EDUCATION 2

3. THE MOLECULAR SIMUL. WORKFLOWNO NO
Is there
a suitable PES? NO
Are ab initio
calculations
available?
Are ab initio
calculations
feasible?
INTERACTION
YES
YES
YES
SUPSIM
Are
dynamics
calculations
direct? NO
Take Force fields from databases
FITTING
Import the
PES routine
YES
YES
DYNAMICS
Exact
quantum
calculations?
Approximate
quantum
calculations? NO NO
Semiclassical
calculations? NO
YES
YES
YES
QDYN
TD / TI
APPROXIMATE
QDYN
SEMICLASSICAL
SC_IVR
QUASI-
CLASSICAL
OBSERVABLES
Fixed J and Energy
Fixed
Energy
Fixed
Temperature NO NO NO
YES
YES
YES
Scalar and vector correlations
Cross-sections
Thermal
Rate coefficients
Thermodynamic properties

4. GEMS flowchart & DATA formats
System input
Q5Cost
Interaction
D5Cost
Dynamics
various
Statistics
Virtual Monitors 4

5. AB INITIO PACKAGES CADPAC Acad Fortran GTO COLUMBUS Acad Fortran GTO
CRYSTAL Acad Fortran GTO
DALTON Acad Fortran GTO
DFT GPL C PW/Wavelet
DIRAC Acad F77, 90, C GTO
GAMESS Acad/Comm Fortran GTO
GAUSSIAN Comm Fortran GTO
MOLCAS Comm Fortran GTO
MOLPRO Comm Fortran GTO
NWChem ECLv F77/C GTO, PW
TERACHEM Comm C/CUDA GTO

6. DATA FORMATS
QC: FIXED GEOMETRY MULTI STATE - SD (Small data) input, parameters, properties -> formatted human readable like XML - LD (Large data) binary working quantities like 4 index integrals IJKL  OPEN BABEL: open, collaborative project allowing search, conversion, analysis, or data storing in CMMST CML: A XML-based format for chemistry HDF5: a hierarchical data model

7. HDF5
° CONTAINERS (groups) domains of quantities defined by common basis functions (AO atomic orbitals, MO molecular orbitals, WF Wave functions, ..) ° METADATA (attributes) simple and small sets of data describing a set of data ° DATA (data ses) large set of binary quantities referring to wavefunction integrals storing in matrices with an arbitrary number of indices ° LIBRARIES (Utilities and tools) Q5dump reports the content of Q5cost files Q5edit python based program text editor

8. Determinants/ coefficients
System
overlap
oneint
twoint
Title
Electrons /a,b AO
Name
Num_orb_sym
Num_orb_tot Labels
Transformation MO
AO_pointer
Num_orb_tot Labels Orbitals SCF_energy
Classification
Occ_num
Symmetry
Ctime (s)
Atime (s)
Q5version (s)
Symmetry:
- num_sym
- labels
densities
Geometry:
- charges
- coordinates
- nuclear_energy
- num_atom
- atomic_number
Basis
Coord system
Atom
Angular number
Magnetic number Coeff/exp
Num of contracted
Num of primitives
prop
Description
Rank
Real/Complex
Index/value WF
MO_pointer
Energy
Core Energy
Num_dets
DetCoeff
Determinants/ coefficients
Energy derivatives
Non adiabatic coupling
Q5 EXTENSION TO SUPPORT D5

9. INSERTION OF Q5/D5 IN GEMS
Fitting
ForceField
SMatrix
QuantumFunction
Trajectories
Spectra
CrossSection
RateCoeffs
System
Interaction
Dynamics
Observables
AbInitio
q5 “file system” +
energy derivatives +
non-ad. coupling els. –
system general info

10. QUANTUM DYNAMICS PACKAGES
ABC
RWAVEPR
FLUSS
MCTDH

11. CLASSICAL DYNAMICS PACKAGES (LARGE SYSTEMS)
VENUS
AMBER
CHARMM
DL_POLY
GROMACS
MOLDY
TINKER
YASARA

12. HTC (square) + HPC CALCULATIONS
SUPSIM MODULE:
HTC (square) + HPC CALCULATIONS

13. THE MCTDH (QDYN) MODULE: HPC (square) + HTC CALCULATIONS

14. THE GRIF SERVICE ORIENTED APPROACH
A registration, access, movement, storage repository of tools, applications and services
A metric to select the computer platform
A simplified and ubiquitous access
A parameterized resource selection
C. Manuali, A. Lagana’
GRIF: A New Collaborative Framework for a Web Service Approach to Grid Empowered Calculations
Future Generation of Computer Systems, 27(3), (2011) DOI /j.future

15. GriF: a framework for grid empowering computational applications
Make grid applications user friendly, black box like and optimize automatically the distribution of tasks over the grid.
Adopt a collaborative JAVA Service Oriented Architecture (SOA) framework articulated as a set of grid services
Provide users with standard operational modalities based on friendly user driven services allowing the composition of one or more services transparently to their implementation details.
Conveniently direct the jobs to the appropriate machine

16. The Basic Architecture of GriF
Scientific Linux Distribution
Service Oriented Architecture
(UDDI, WSDL, SOAP)
UDDI4J, WSDL4J, AXIS
Java Web Services
(JWS)
Tomcat Web Server
MySQL DBMS
Java Swing/AWT
(platform-independent client)
COMPCHEM Virtual Organization - GriF

17. The Extended Architecture of GriF for bridging HTC and HPC
HPC: GriF has been extended to offer to the Grid users the possibility of running their Grid applications (serial, parallel: MPI/OpenMP) on some HPC platforms by bridging the corresponding HPC facilities directly.
COMPCHEM Virtual Organization - GriF

18. Preliminary HPC/HTC Case Studies
In particular, Grid Applications can be run from GriF to HPC either under the form of ‘Service’ (programs already made available by GriF for running on HPC) or, more in general, by uploading user customized binaries.
Serial:
a) ABC. Implemented as a COMPCHEM Service.
Parallel (supporting MPI & OpenMP libraries):
a) ADF. Implemented as a HPC Service (MPI);
b) GAMESS-US. Implemented as a HPC Service (MPI);
c) POMP. Implemented as a HPC Service (OpenMP).
Therefore, by GriF one can manage the corresponding generated HPC jobs (e.g. status checking, deletion) retrieving related results (under the form of a compressed zip package).
COMPCHEM Virtual Organization - GriF

19. General Capabilities (1/2)
Provides Single Sign-On for all the Grid-related operations (users only need to be registered in GriF)
No need for managing Grid Certificates, Jobs Id nor the command-line
Application runs offered as Grid Services efficiently
Supports Multiple Input and Output for all the Grid executions
Supports Single and Parameter Study running modalities as well as Parametrized Workflows
Provides jobs description and advanced management (e.g. subjobs re-scheduling)
COMPCHEM Virtual Organization - GriF

20. General Capabilities (2/2)
7. Optimizes results gathering (in terms of time and space)
Supports Mobile Devices (Google Android, Apple iOS)
Provides automatic notifications for ‘done’ jobs and user feedbacks
Provides Computing Element Queues Ranking
Supports a Quality Credits/Costs Schema (by providing data for the so called Quality of Service (QoS) and Quality of User (QoU) global evaluation parameters developed by the COMPCHEM VO for estimating its activities)
General Capabilities (2/2)
COMPCHEM Virtual Organization - GriF

21. GRID PLATFORMS OFFER AN ALTERNATIVE SCHEME FOR ON DEMAND COMPUTING (RESOURCES (HPC+HTC) AND TOOLS SHARING) FOR THE CHEMISTRY COMMUNITY
VIRTUAL RESEARCH COMMUNITIES OFFER A SOLID GROUND TO COLLABORATIVE COMPUTING METRICS (QUALITY EVALUATION)
VIRTUAL RESEARCH COMMUNITIES CAN SUPPORT A SUSTAINABILITY PROOF ECONOMY
CONCLUSIONS
COMPCHEM Virtual Organization - GriF